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UniProtKB - P0AFK9 (POTD_ECOLI)

Entry version 109 (13 Nov 2019)
Sequence version 1 (20 Dec 2005)
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Protein

Spermidine/putrescine-binding periplasmic protein

Gene

potD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei36Spermidine1 Publication1
Binding sitei85Spermidine1 Publication1
Binding sitei327Spermidine1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processTransport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:POTD-MONOMER
ECOL316407:JW1109-MONOMER
MetaCyc:POTD-MONOMER

Protein family/group databases

Transport Classification Database

More...TCDBi		3.A.1.11.1 the atp-binding cassette (abc) superfamily

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Spermidine/putrescine-binding periplasmic protein
Short name:
SPBP
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:potD
Ordered Locus Names:b1123, JW1109
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

  • Periplasm 1 Publication

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Periplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Chemistry databases

Drug and drug target database

More...DrugBanki		DB03566 Spermidine

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 233 PublicationsAdd BLAST23
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000003183724 – 348Spermidine/putrescine-binding periplasmic proteinAdd BLAST325

Proteomic databases

Encyclopedia of Proteome Dynamics

More...EPDi		P0AFK9

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0AFK9

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P0AFK9

PRoteomics IDEntifications database

More...PRIDEi		P0AFK9

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...SWISS-2DPAGEi		P0AFK9

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4261797, 57 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-4383 Spermidine ABC transporter complex

Protein interaction database and analysis system

More...IntActi		P0AFK9, 7 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1123

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1348
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P0AFK9

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P0AFK9

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni168 – 171Spermidine-binding1 Publication4

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the bacterial solute-binding protein PotD/PotF family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4107RUE Bacteria
COG0687 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000263814

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0AFK9

KEGG Orthology (KO)

More...KOi		K11069

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0AFK9

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR006059 SBP
IPR001188 Sperm_putr-bd

Pfam protein domain database

More...Pfami		View protein in Pfam
PF13416 SBP_bac_8, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF019574 Periplasmic_polyamine_BP, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00909 SPERMDNBNDNG

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P0AFK9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET 
        60         70         80         90        100
GIKVIYSTYE SNETMYAKLK TYKDGAYDLV VPSTYYVDKM RKEGMIQKID 
       110        120        130        140        150
KSKLTNFSNL DPDMLNKPFD PNNDYSIPYI WGATAIGVNG DAVDPKSVTS 
       160        170        180        190        200
WADLWKPEYK GSLLLTDDAR EVFQMALRKL GYSGNTTDPK EIEAAYNELK 
       210        220        230        240        250
KLMPNVAAFN SDNPANPYME GEVNLGMIWN GSAFVARQAG TPIDVVWPKE 
       260        270        280        290        300
GGIFWMDSLA IPANAKNKEG ALKLINFLLR PDVAKQVAET IGYPTPNLAA 
       310        320        330        340 
RKLLSPEVAN DKTLYPDAET IKNGEWQNDV GAASSIYEEY YQKLKAGR
Length:348
Mass (Da):38,867
Last modified:December 20, 2005 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i1E6EB7A6B4EC63AB
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
M64519 Genomic DNA Translation: AAC37041.1
U00096 Genomic DNA Translation: AAC74207.1
AP009048 Genomic DNA Translation: BAA35943.1

Protein sequence database of the Protein Information Resource

More...PIRi		D40840

NCBI Reference Sequences

More...RefSeqi		NP_415641.1, NC_000913.3
WP_000759317.1, NZ_STEB01000016.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74207; AAC74207; b1123
BAA35943; BAA35943; BAA35943

Database of genes from NCBI RefSeq genomes

More...GeneIDi		945682

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1109
eco:b1123

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.1144

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64519 Genomic DNA Translation: AAC37041.1
U00096 Genomic DNA Translation: AAC74207.1
AP009048 Genomic DNA Translation: BAA35943.1
PIRiD40840
RefSeqiNP_415641.1, NC_000913.3
WP_000759317.1, NZ_STEB01000016.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1POTX-ray1.80A24-348[»]
1POYX-ray2.501/2/3/426-348[»]
SMRiP0AFK9
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261797, 57 interactors
ComplexPortaliCPX-4383 Spermidine ABC transporter complex
IntActiP0AFK9, 7 interactors
STRINGi511145.b1123

Chemistry databases

DrugBankiDB03566 Spermidine

Protein family/group databases

TCDBi3.A.1.11.1 the atp-binding cassette (abc) superfamily

2D gel databases

SWISS-2DPAGEiP0AFK9

Proteomic databases

EPDiP0AFK9
jPOSTiP0AFK9
PaxDbiP0AFK9
PRIDEiP0AFK9

Genome annotation databases

EnsemblBacteriaiAAC74207; AAC74207; b1123
BAA35943; BAA35943; BAA35943
GeneIDi945682
KEGGiecj:JW1109
eco:b1123
PATRICifig|1411691.4.peg.1144

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB0745

Phylogenomic databases

eggNOGiENOG4107RUE Bacteria
COG0687 LUCA
HOGENOMiHOG000263814
InParanoidiP0AFK9
KOiK11069
PhylomeDBiP0AFK9

Enzyme and pathway databases

BioCyciEcoCyc:POTD-MONOMER
ECOL316407:JW1109-MONOMER
MetaCyc:POTD-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AFK9

Protein Ontology

More...PROi		PR:P0AFK9

Family and domain databases

InterProiView protein in InterPro
IPR006059 SBP
IPR001188 Sperm_putr-bd
PfamiView protein in Pfam
PF13416 SBP_bac_8, 1 hit
PIRSFiPIRSF019574 Periplasmic_polyamine_BP, 1 hit
PRINTSiPR00909 SPERMDNBNDNG

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPOTD_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0AFK9
Secondary accession number(s): P23861
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: November 13, 2019
This is version 109 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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